If someone has access to the same spell at two different levels, is it possible for them to gain the spell twice? Giving them the ability to choose between casting the spell at a lower spell slot or casting it with a higher DC. As an example, the whispering way faction in the faction guide lets you learn necromancy spells at a lower level. The example in the book is a 3rd level Enervation spell (normally 4th level). Can someone learn the 3rd level version and cast it as a 3rd level spell (DC 13+ability mod) and also learn it as a 4th level spell (DC 14+ability mod)?
It would depend on the wording of the ability that is letting you learn the spell at a lower level. If the ability says can learn or something similar than the answer is yes. If on the other hand it says something like learns spells at one level lower than that answer is no. That is of course the RAW answer, the real answer is ask your GM.